The ballots contained nominations from industry companies and professionals. To be eligible for an award, anime or manga must be available in the U.S. during the previous year, prior to the awards gala. Whether by DVD (or book or periodical, in the case of manga), national TV, or theatrical release. Anime and manga are defined, as animation or comics, respectively, originally produced in Japan.

Voting was conducted via an online ballot system. The American Anime Awards partnered with respected industry news site ICv2 to host and track the fan voting to ensure accurate voting and to eliminate any mass voting by single individuals. Fans cast their votes at www.americananimeawards.com starting on January 1, 2007 and ending on January 31, 2007.

The nominating and voting process has received criticism from fans for lack of clarity and being too inclusive: for example, while some acting nominees are specifically cited for one or more series, others are cited for none at all, leaving it to the voter to decide if they should consider the series specifically mentioned, or the actor's entire body of work. Also, since evidently any anime that was released in any way in 2006 is eligible for nomination, some actors have been nominated for work done years or even decades ago. Another criticism was the apparent error of including Johnny Yong Bosch as Best Actor in a Comedy despite the fact Akira is not a comedy.